EMBL-EBI MSD Search and Visualization tools Jawahar Swaminathan

EMBL-EBI Issues  The raw database is large and complex: 27,190+ PDB entries 120+ tables in the warehouse, many very large Cross-referenced against UniProt, PubMed...  Need to expose as much of the data as possible, without making the interface too complex  We want to cater for three categories of user: "Novice" user Experienced user Expert user

EMBL-EBI biobar A toolbar search application for Mozilla/Netscape or firefox browsers

EMBL-EBI Biobar ( )

EMBL-EBI biobar  All major bioinformatics databases covered.  Search genomic, proteomic, structural, literature and functional databases.  Links to deposition and analysis tools for sequence and structural data.

EMBL-EBI MSDlite A simple form-based query system to search the MSD Databases

EMBL-EBI MSDlite

EMBL-EBI MSDlite

EMBL-EBI The Atlas Pages

EMBL-EBI The Atlas: Ligands

EMBL-EBI The Atlas: Sequence

EMBL-EBI  View structures as wireframe, backbone or ribbons  Built-in sequence viewer  Calculate and display surfaces  Various display options:  Ramachandran plots  Distance matrix  B-factors Based on the AstexViewer™ from Astex Technology Limited and modified under licence by the MSD group

EMBL-EBI  Strengths:  simple, easy to use form  allows multiple search fields to be combined  relatively fast, despite performing quite complex SQL queries  Weaknesses:  not exposing the power of a relational database  user can't specify the relationship between search fields:  "name" AND "title" AND "keyword"  "name" OR "title" OR "keyword"  ( "name" OR "title" ) AND NOT "keyword"  the search form is defined by the authors of the search system, not the author of a query Simple search interface

EMBL-EBI Describing complex searches  We want to allow the user to entirely control their query  Since HTML forms are inherently static, we'll use an applet to provide a dynamic "form" that will let the user:  choose the fields to be searched  specify the relationships between search fields  choose the result fields and how results are presented  perform "complex" sub-queries e.g. SSM, FASTA

EMBL-EBI A graphical database search system  MSDpro uses an applet for constructing queries and a server to execute them  Avoids the need for the user to understand a complex database schema or know SQL  The user describes their query entirely graphically, including logical operations such as AND, OR and NOT  Applet generates an XML description of the user’s query, which is sent to the MSD query server and converted to SQL automatically

EMBL-EBI MSDpro A flexible graphical search interface for advanced searching

EMBL-EBI

EMBL-EBI

EMBL-EBI Automatic SQL query generation  The query server is a Java servlet:  accepts a query description as XML  converts the user’s query description into a true SQL query, which is then submitted to the search database  Searches can include components that are executed outside of the database, e.g. sequence similarity, determined using FASTA or structural similarity, determined using SSM

EMBL-EBI Search system is generic  The search system is designed to be entirely database-independent  All information about the architecture of the search database is stored in XML dictionaries  Similarly, the search and result fields which the applet presents to the user are controlled by a dictionary  The entire system could move to a completely different database simply by modifying the dictionaries

EMBL-EBI Java server

EMBL-EBI Java server architecture User interface Methods Interface Ontology DB DB and external object ontology Methods

EMBL-EBI Web-services Some of the new services from MSD are designed as web-services:  web-services are network-based services with published method signatures  can be accessed via the SOAP protocol from any language with a SOAP library, via http  The same services used within MSDpro will be accessible to any SOAP client  The MSD query engine will also be available as a web-service, allowing users to submit queries programmatically

EMBL-EBI

EMBL-EBI Query generation

EMBL-EBI Query generation SQL > select from where B,C,E Fragments of C A,BB,D “C” - external B A = selection B = DB objects C = Query D = table joins E = plugin description